ckandoth / variant-filter
A false-positive filter for variants called from massively parallel sequencing
☆29Updated 7 years ago
Related projects ⓘ
Alternatives and complementary repositories for variant-filter
- An awk-like VCF parser☆55Updated 10 months ago
- utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.☆48Updated 5 years ago
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆50Updated 4 years ago
- ☆45Updated 5 years ago
- R package for inferring copy number from read depth☆31Updated 2 years ago
- QDNAseq package for Bioconductor☆49Updated 3 months ago
- Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…☆51Updated 7 years ago
- Documenting usage and experience with bioinformatic tools☆40Updated 9 years ago
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆21Updated 2 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Burden testing against public controls☆50Updated 8 months ago
- Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of func…☆24Updated 10 months ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆69Updated 4 years ago
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆45Updated 6 years ago
- Full-spectrum copy number variation detection by high-throughput DNA sequencing☆37Updated 3 years ago
- ☆78Updated 10 years ago
- CNV screening and annotation tool☆24Updated 8 years ago
- identifying mutational significance in cancer genomes☆60Updated 2 years ago
- CN-Learn☆29Updated 4 years ago
- A tool for simulating CNVs for WES data. It simulates rearranged genome(s), short reads (fastq) and BAM file(s) automatically in one sing…☆18Updated 4 years ago
- R package designed to simplify structural variant analysis☆70Updated 2 years ago
- ☆67Updated 2 years ago
- Quality of RNA-Seq Toolset☆52Updated 5 years ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆49Updated 2 years ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆76Updated 4 years ago
- Concordance and contamination estimator for tumor–normal pairs☆56Updated last month
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆94Updated 3 years ago
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Updated last year
- BIC@MSKCC Variants Pipeline☆23Updated last year